Natural-product-based fluorescent probes: recent advances and applications

Abstract

Fluorescent probes are attractive tools for biology, drug discovery, disease diagnosis, and environmental analysis. In bioimaging, these easy-to-operate and inexpensive probes can be used to detect biological substances, obtain detailed...

Biochemical Discovery, Intracellular Evaluation, and Crystallographic Characterization of Synthetic and Natural Product Adenosine 3′,5′-Cyclic Monophosphate-Dependent Protein Kinase A (PKA) Inhibitors

“…A common challenge in natural product discovery screens with a fluorescence-dependent signal can be an increased false-positive rate due to fluorescence interference. Many highly absorptive dyes and fluorescent probes are derived from or are themselves natural products, and therefore when screening libraries of natural product extracts, these compounds can commonly be encountered as fluorescence-interfering false-positive hits. , In our experience, one way to reduce the likelihood of fluorescence interference is to design the assay so that a wash step can be incorporated prior to signal generation (reducing signal interference from the library components). , In order to incorporate this wash step, we have chosen a modified sandwich enzyme-linked immuno-sorbent assay (ELISA) as our screening assay format. For this kinase assay, we chose to use the RIα 2 :J-PKAcα 2 holoenzyme as the source of kinase activity in order to allow us to potentially find inhibitory compounds which may stabilize the inactive holoenzyme as a possible mechanism of action.…”

“…Many highly absorptive dyes and fluorescent probes are derived from or are themselves natural products, and therefore when screening libraries of natural product extracts, these compounds can commonly be encountered as fluorescence-interfering false-positive hits. 26,27 In our experience, one way to reduce the likelihood of fluorescence interference is to design the assay so that a wash step can be incorporated prior to signal generation (reducing signal interference from the library components). 28,29 In order to incorporate this wash step, we have chosen a modified sandwich enzyme-linked immuno-sorbent assay (ELISA) as our screening assay format.…”

Fluorimetric Cell Analysis with 9‐Aryl‐Substituted Berberine Derivatives as DNA‐Targeting Fluorescent Probes

“…To combine these desired properties in fluorescent probes, core structures from established fluorescent natural products have been employed, considering that their biological origin may support biocompatibility. Thus, natural product derivatives based on the heteroaromatic alkaloids coralyne [6] and berberine [7] have been used as lead structure of DNA‐targeting fluorescent probes because they have high binding affinity and selectivity towards specific DNA forms [1c,g,8] . In particular, berberine ( 1 a ) has high bioactivity, as well as reasonable binding affinities to different DNA forms, for example duplex, triplex or quadruplex DNA [9]…”

“…But notably, this light‐up effect does not clearly correlate with the DNA‐binding properties of berberine [11] . Therefore, it is desirable to further functionalize the berberine scaffold with substituents that have a more predictable influence on the emission properties and that, in turn, may govern the extent of the DNA‐sensitive fluorescence light‐up effect [1c,7,11] . In this regard, it has been shown already that additional aryl groups at the berberine core quench the fluorescence intensity by a non‐radiative deactivation of the excited state by torsional relaxation in aqueous solution [11,12] .…”

“…In this regard, it has been shown already that additional aryl groups at the berberine core quench the fluorescence intensity by a non‐radiative deactivation of the excited state by torsional relaxation in aqueous solution [11,12] . In the confined medium of a DNA binding site, however, these conformational changes are sterically hindered, which leads to an increased emission quantum yield of the bound ligand [1b,c,g] . This fluorescence light‐up effect depends on the binding site and the binding mode with the DNA host molecule because these factors have an influence on the rotational freedom and the torsional angle about the biaryl axis [12] .…”